Exercise training is well known to affect a suite of physiological and performance traits in mammals, but effects of training in other vertebrate tetrapod groups have been inconsistent. We examined performance and physiological differences among green anole lizards (Anolis carolinensis) that were trained for sprinting or endurance, using an increasingly rigorous training regimen over 8 weeks. Lizards trained for endurance had significantly higher post-training endurance capacity compared to the other treatment groups, but groups did not show post-training differences in sprint speed. Although acclimation to the laboratory environment and training explain some of our results, mechanistic explanations for these results correspond with the observed performance differences. After training, endurance-trained lizards had higher hematocrit and larger fast glycolytic muscle fibres. Despite no detectable change in maximal performance of sprint-trained lizards, we detected that they had significantly larger slow oxidative muscle fibre areas compared to the other treatments. Treatment groups did not differ in the proportion of number of fibre types, nor in the mass of most limb muscles or the heart. Our results offer some caveats for investigators conducting training research on non-model organisms, and they reveal that muscle plasticity in response to training may be widespread phylogenetically.